Den Dekker was a second-team All-State pick in high school in 2006 after hitting .455 with 7 home runs. As a freshman at the University of Florida, he batted .234/~.324/.418. Matt was much better as a sophomore, hitting .333/~.413/.507 with 20 steals in 20 tries and 55 runs in 55 games. The center fielder was a first-team All-Southeastern Conference pick in the outfield. Den Dekker was then chosen for Team USA's college edition. He batted .176/.375/.176 in the 2008 Haarlem Baseball Week; noted for his defense, he made one error and noted for his speed, he was thrown out in his lone attempt (gunned down by Cuban defensive legend Ariel Pestano in the Gold Medal game). Den Dekker batted .227/.292/.409 in the 2008 World University Championship and did not attempt a steal. In the Gold Medal game, he almost drove in the winner, singling in the 12th, but Tommy Mendonca was gunned down at home by Keijiro Matsumoto.

Matt's stock fell drastically as a junior, when he hit .296/.409/.412 with 17 steals in 18 tries. He was still rated 92nd overall by Baseball America among prospects entering the 2009 amateur draft - then was not selected until the 475th overall pick, when the Pittsburgh Pirates snatched him in the 16th round. He returned to Florida for his senior year, hitting .358 with a team-leading 64 runs scored and a career-best 49 RBI as his school reached the 2010 College World Series.

After college, den Dekker was selected by the New York Mets in the fifth round of the 2010 amateur draft. The scout was Les Parker. He made his pro debut that summer with the GCL Mets, hitting .278 with 5 RBI in 5 games before being promoted to the Savannah Sand Gnats, for whom he batted .346/.404/.471 with 21 runs in 27 games. In 2011, he played for the St. Lucie Mets (.296/.362/.494, 8 3B, 54 R in 67 G) and the Binghamton Mets (.235/.312/.426 in 72 G). For the year, he had 103 runs, 32 doubles, 11 triples, 17 home runs and 24 steals in 34 tries. He tied Kentrail Davis for 4th in the Florida State League in three-baggers despite only half a season there. He easily led the Mets chain in runs (26 ahead of #2 Josh Satin), tied Jordany Valdespin for second in doubles (behind Satin), was second in triples, tied Valdespin and Aderlin Rodriguez for fourth in home runs, led in total bases (248, 9 ahead of Valdespin) and was 5th in steals while fielding .993 for a very good all-around performance.

In 2012, Matt remained productive with Binghamton (.340/.397/.563, 47 R in 58 G), though he fell to .220/.256/.373 in 77 games for the Buffalo Bisons. For the season, he scored 84 runs, drove in 76, had 31 doubles, 8 triples, 17 home runs and 21 steals in 30 tries. He fielded .985 with 11 assists. He led the Mets farm system in runs (4 ahead of Fred Lewis), was third in hits, was second in doubles (four shy of Dustin Lawley), led in triples, tied Val Pascucci for 5th in dingers, tied Cory Vaughn and Juan Lagares for 5th in swipes, led in total bases again (244, 8 more than Wilmer Flores) and was second to Rodriguez in RBI.